Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

Skvortsov, Timofey; Leeuwe, Colin de; Quinn, John P.; McGrath, John W.; Allen, Christopher C. R.; McElarney, Y.; Watson, C. J.; Arkhipova, Ksenia; Lavigne, Rob; Kulakov, Leonid

doi:10.1371/journal.pone.0150361

Cited by 74 publications

(77 citation statements)

References 64 publications

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“…In this geospatial metagenomics study, we identified virome abundance and diversity in different reservoirs and tributaries. Due to insufficient viral genome sequencing information in the NCBI, 41.4% of the virome genome had no significant hits and bacteriophages were the most abundant organisms in the matrix, which is in agreement with previous studies of surface water viromes (Mohiuddin and Schellhorn, 2015;Skvortsov et al, 2016;Tseng et al, 2013). Phages, considered to be the most abundant and diverse biological entities on Earth, play an important role in shaping biological and geochemical processes at the global scale (Díaz-Muñoz and Koskella, 2014).…”

Section: Geospatial Distribution Of Viromesupporting

confidence: 87%

“…Determining the factors in constructing the viral community is important for both understanding and manipulating ecosystems (Dinsdale et al, 2008). Factors shaping the viral community in freshwater ecosystems can include temporal factors, geospatial factors, natural disturbances (e.g., typhoon) and human activities (Djikeng et al, 2009;Emerson et al, 2012;Fancello et al, 2013;Ge et al, 2013;Hwang et al, 2017;L opez-Bueno et al, 2009;Skvortsov et al, 2016;Tseng et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Geospatial distribution of viromes in tropical freshwater ecosystems

Tay

et al. 2018

Water Research

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This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.

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Section: Geospatial Distribution Of Viromesupporting

confidence: 87%

Section: Introductionmentioning

confidence: 99%

Geospatial distribution of viromes in tropical freshwater ecosystems

Tay

et al. 2018

Water Research

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“…Elucidating such predominant virus-host interactions is key to characterizing viruses playing central roles in the microbial ecosystem and biogeochemical cycling. However, despite a growing number of viromic studies in freshwater systems (Skvortsov et al, 2016;Moon et al, 2017;Silva et al, 2017;Arkhipova et al, 2018), viruses infecting other typical freshwater bacterioplankton lineages, such as LD12 (Ca. Fonsibacter) (Henson et al, 2018) and Limnohabitans (Kasalický et al, 2013) have yet to be characterized.…”

Section: Introductionmentioning

confidence: 99%

Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

Okazaki

Nishimura

Yoshida

et al. 2019

Environmental Microbiology

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Summary Metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22–5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome‐assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur‐limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters.

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“…Although viral taxa have been continuously updated by the virus research community1011, there are still many misclassifications in the ICTV viral taxonomy12, as well as many viral families currently not included in the RefSeq database. Further, the sequencing of viral metagenomic samples often results in many viral genomes that are of unknown origin1314.…”

mentioning

confidence: 99%

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

Zhang

Jun

Leuze

et al. 2017

Sci Rep

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The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral “tree of life”. However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.

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Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

Cited by 74 publications

References 64 publications

Geospatial distribution of viromes in tropical freshwater ecosystems

Geospatial distribution of viromes in tropical freshwater ecosystems

Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

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